I basically have the footer turned off, no functions or decoration, except for single post pages. This shows well in Google/Firefox (does leave white space) but in IE it shows it still there with background and full width.

On both sites:

http://www.theblogfarm.com/
http://www.thejeffersontree.com/

Is there any way to turn off footers on everything except single post pages? Or at least make it invisible on IE?

It seems I remember you had some special styling for the footer as they weren't displaying correctly. That is probably impacting how they are now showing. I would look back at that code.

Also you say you "basically have the footer turned off". Does that mean you have those footer boxes empty?

Edit: This is the 'post' footer I am talking about.

Yes, footer boxes are empty and no functions (info items) on footer except on single post pages.
The code was for menu transparency which I pasted below. That shouldn't affect anything. I did add a height code for the header to make it show right in IE, but boxes for styling footer are empty.

IE is showing border and backgound image, both of which are removed?

Edit: I just noticed in IE the single pages are showing the footer properly, just the main page. author and category pages show a footer.

#menu1 {
border: solid 1px #4D5232 !important;
background: url(/wp-content/themes/atahualpa351/images/sidebarbg04.jpg) repeat top left;
box-shadow: 0 0 10px #333;
-moz-box-shadow: 0 0 10px #333;
-moz-border-radius:5px;
-khtml-border-radius: 5px;
-webkit-border-radius:5px;
border-radius: 5px;
}
div#menu1 ul.rMenu {
background: transparent;
}

div#menu1 ul.rMenu li {
background-color: transparent;
}
div#menu1 ul.rMenu li.current_page_item a:link,
div#menu1 ul.rMenu li.current_page_item a:active,
div#menu1 ul.rMenu li.current_page_item a:hover,
div#menu1 ul.rMenu li.current_page_item a:visited,

div#menu1 ul.rMenu li a:hover {
background-color: transparent;
}

div#menu1 ul.rMenu li:hover,div#menu1 ul.rMenu li.sfhover {
background:transparent;
}

I found this page: http://forum.bytesforall.com/showthread.php?t=5515

I tried adding the code into the loop as JD advised without success. This is so weird...

Makes the front pages on both sites look like crap in IE. Any other ideas?

I am wondering if this has something to do with your version of Atahualpa. You might try uploading 3.7.1 into its own folder to test.

I have noticed certain advantages to upgrading, such as 'infinite scroll' and'shadow box' working better in IE on my site that is 3.7.1. To be honest the site is fairly busy and I am concerned there might be problems during upgrade... If I update I will lose all customization, wont I?

I ALWAYS do a manual upgrade. The only things you have to do after uploading 3.7.1 into its own atahualpa371 folder is to copy the header, logo, etc images into the new location and then change any paths in the theme options that include the atahualpa folder. There are instructions for a manual upgrade in the New versions and upgrading forum.

By doing the manual upgrade if something isn't quite right you can just go back to the version you were on.

What about widgets? I have special widgets in footer for links, header for image and login, and loop for featurific?

That will indeed be a problem with the loop.

You could try Atahualpa 3.5.3. Not sure if it will fix your problem though.

I actually like the loop, comes in handy. I tried the tree with 3.5.3 and didn't change anything. There has to be a fix for this, it does not look good.

I saw this: http://forum.bytesforall.com/showthread.php?t=5515 and thought it might work, tried it, didn't. But there is a chance I did not do it correctly. Should this work?

Is there any other way to make the footer not show on the main page? Why would it work fine in Chrome and Firefox and not IE. How can it still show a background and border when there is none specified?

Could it be related to tables or forms in any way? nah, didn't think so... just reaching for straws.

Okay, I gave up... Just added 'Leave a comment' and made the style transparent. Beats worrying about it. Thanks guys.